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Guide to Choosing the Best Water Pump for Aquaponics

When it comes to building a successful aquaponics system, most beginners focus on fish, plants, or grow beds and overlook one critical component: the water pump.

But here’s the truth:

A poorly chosen water pump can quietly sabotage your entire setup. It may not move enough water, causing ammonia to accumulate in your fish tank. Or it might push too much, flooding your grow beds and stressing your plants. Worse, it could fail suddenly, leaving your system dry and your fish gasping.

That’s why choosing the right pump is an important decision that can affect water circulation, oxygenation, filtration, and the health of every living part of your aquaponics ecosystem.

The good news? You don’t need to be a plumber or engineer to get it right.
This beginner-friendly guide will walk you through:

  • What a pump does in an aquaponics system
  • How to calculate the right size
  • What features matter (and which are marketing fluff)
  • The best pumps for small and mid-size systems
  • And how to avoid the most common and costly mistakes

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If you want to skip the trial and error and learn how to build a thriving aquaponics system, from pump sizing to full plumbing layouts, check this 5-hour premium video course just for you.

What Does a Water Pump Do in an Aquaponics System?

The pump moves water from the fish tank to the grow beds, where plants absorb nutrients from fish waste. Afterward, the water drains, usually via gravity, back into the fish tank or a sump tank for recirculation.

This closed-loop circulation:

  • Delivers nutrient-rich water to plants
  • Helps oxygenate water for fish
  • Supports beneficial bacteria for biofiltration
  • Prevents stagnation and harmful ammonia buildup

This process is what makes aquaponics so efficient and sustainable, and the pump is what powers it all.

Where the Pump Fits in Your Setup

There are a few common aquaponics layouts, but here’s a basic example of where the pump typically sits:

[Fish Tank] → (Pump) → [Grow Bed] → (Drain via gravity) → [Sump Tank or Fish Tank]

Water Pump Placement in Aquaponics

Tip:In small backyard or desktop systems, the pump is often located directly in the fish tank (submersible style). In larger or more complex builds, an inline pump located in a sump tank may be more efficient.

Factors to Consider When Choosing a Water Pump

Not all water pumps are created equal. To keep your aquaponics system running smoothly, you’ll need a pump that delivers the right amount of flow, handles your system’s layout, and won’t drain your power bill.Here’s what to look for when choosing the water pump for your system.

1. Flow Rate (GPH)

Gallons Per Hour (GPH) tells you how much water the pump can move in one hour. For most aquaponics systems, a good rule of thumb is to circulate the entire volume of your fish tank once every hour.

Example:

  • If your fish tank holds 100 gallons, aim for a pump rated at least 100 GPH, but preferably 25–50% more to account for flow loss.
  • Flow rate sweet spot: 1–1.5x your fish tank volume per hour

2. Head Height (or Head Pressure)

This measures how high your pump can push water vertically,  and it’s often overlooked.The more height and resistance your pump has to overcome (pipes, filters, elbows), the lower the actual flow becomes. This is where many beginners underpower their systems.

Tip:Always check the flow chart provided by the manufacturer as it shows how much flow the pump delivers at different head heights (e.g., 1ft, 3ft, 5ft).

3. Energy Efficiency

Because your pump runs 24/7, energy use matters. Look for models labeled energy-efficient or with low wattage draw.

Consider:

  • Wattage (lower is better for small systems)
  • Daily and monthly operating costs
  • Whether your region supports solar backup or off-grid options

4. Submersible vs Inline Pumps

Both can work in aquaponics, but they suit different system types:

Type

Ideal For

Pros

Cons

Submersible

Small to medium backyard systems

Easy to install, quieter

Limited head height, heats water

Inline

Large or commercial systems

Powerful, cooler, scalable

Requires external plumbing

 

Recommendation:For most beginners, a submersible pump rated for aquariums or hydroponics is a great starting point.

5. Durability & Brand Reputation

Look for pumps that are:

  • Fish-safe (no oil-based components)
  • Corrosion-resistant (especially in systems with high humidity)
  • Backed by a warranty or return policy
  • Well-reviewed in aquaponics or hydroponic forums

6. Your System’s Design

Every aquaponics system is different. Consider:

  • Do you use a sump tank?
  • Are your grow beds above or beside the fish tank?
  • Are you running a constant flood or flood-and-drain system?

Common Water Pump Mistakes Beginners Make and How to Avoid Them

Below are the most common pump mistakes in aquaponics and how to avoid them.

1. Choosing the Wrong Size Pump

Most new growers either:

  • Undersize the pump (leading to poor water flow and oxygen issues), or
  • Oversize it (which creates turbulence, disturbs fish, and wastes energy)

What to do instead:

  • Use the 1–1.5x tank turnover rule, and always factor in head height losses.

2. Ignoring Head Height & Plumbing Losses

Pumps rarely deliver their rated GPH in real-world conditions. Every vertical lift, bend, elbow, or valve adds resistance and lowers flow.

Solution:

  • Map out your system plumbing
  • Add 1 foot of head height per 10 feet of horizontal pipe or each 90° elbow
  • Choose a pump with extra capacity to compensate

3. Running the Pump on a Bad Power Source

Power fluctuations or outages can fry a pump or cause total system failure, especially overnight.

Tip:

  • Use a surge protector and GFCI outlet
  • Consider a battery backup or solar system if you're in a rural or blackout-prone area

4. Using the Wrong Type of Pump

Not all pumps are suitable for aquaponics:

  • Fountain pumps can clog easily or lack power
  • Cheap pond pumps may overheat or contain oils harmful to fish

Look for:

  • Aquarium-grade or hydroponic pumps-safe materials
  • Fish-safe materials
  • Continuous-duty rated models

5. No Maintenance Plan

Over time, algae, fish waste, or debris can clog your pump’s intake which can reduce flow or burn out the motor.

Maintenance Tip:

  • Clean the filter/screen every 2–4 weeks
  • Visually inspect tubing and fittings
  • Replace pumps every 12–24 months, depending on brand

The Best Water Pumps for Aquaponics 

When it comes to aquaponics, choosing a reliable water pump is more than just picking a name brand. You want a pump that’s quiet, efficient, durable, fish-safe and most importantly, suited to your specific system size.

Below are 5 beginner-friendly water pumps that are trusted by aquaponics growers, including brands we’ve tested in our own systems.

EcoPlus Water Pump

1. EcoPlus Submersible Water Pump (Eco 396 – 594 GPH)

Best for: Small backyard or indoor systems (20–80 gallons)
Specs:

  • Flow Rate:396 GPH
  • Max Head Height:6.5 ft
  • Wattage: 36W
  • Type: Submersible

Pros:

  • Affordable and reliable
  • Quiet operation
  • Comes with multiple outlet fittings

Cons:

  • Not ideal for larger or multi-bed systems
  • Plastic housing requires gentle handling
Active Aqua 550 GPH Water Pump

2. Active Aqua Submersible Pump (550 GPH)

Best for: Mid-size systems with 50–100 gallons
Specs:

  • Flow Rate: 550 GPH
  • Max Head Height:7.5 ft
  • Wattage:32W

Pros:

  • Energy-efficient
  • Comes with a pre-filter sponge
  • UL-listed and widely used in hydro setups

Cons:

  • Slightly bulky for tight spaces
  • Pre-filter may clog faster in high-solids systems

 

Jebao DCT Marine Controllable Water Pump

3. Jebao DCT Series Inline Pump (Variable Speed – 1056+ GPH)

Best for: Larger systems or users wanting high control
Specs:

  • Flow Rate:Adjustable up to 1056 GPH
  • Max Head Height:10–13 ft
  • Type: Inline (external)

Pros:

  • Quiet, powerful, and adjustable
  • Digital controller
  • Great for future expansion

Cons:

  • Requires external plumbing setup
  • Not fully submersible

 

Simple Deluxe 60W 800GPH Submersible Pump

4. Simple Deluxe Submersible Pump (400–1056 GPH Range)

Best for: Budget-conscious beginners with small to mid-sized systems
Specs (400 GPH model):

  • Flow Rate:400 GPH
  • Head Height: 6.9 ft
  • Wattage: ~35W

Pros:

  • Budget-friendly
  • Multiple sizes to choose from
  • Decent warranty

Cons:

  • May require more frequent cleaning
  • Mixed long-term durability reviews

 

Danner Supreme Magnetic Drive Pumps

5. Danner Supreme Aqua-Mag Magnetic Drive Pump

Best for: High-performance systems requiring durability
Specs (Model 5):

  • Flow Rate: 500 GPH
  • Head Height: 10 ft
  • Type: Inline or Submersible (dual use)

Pros:

  • Magnetic drive = quiet & energy efficient
  • Long-lasting build
  • Trusted by commercial aquaponics farms

Cons:

  • More expensive than other beginner options
Aquaponics System

Frequently Asked Questions About Aquaponics Pumps

Here are some of the most common questions beginners ask with clear, concise answers you can trust.

1. How long should I run my water pump each day?

Answer:In most aquaponics systems, the pump should run 24/7.
Constant water circulation ensures:

  • Oxygen-rich water for fish
  • Consistent nutrient delivery to plants
  • Stable biofiltration by beneficial bacteria

Exception: If you're using a timer-based flood-and-drain system, the pump may cycle on/off every 15–30 minutes.

2. What size pump do I need for aquaponics?

Answer:Choose a pump that can turn over your fish tank’s total volume once every hour, plus an extra 25–50% to account for head height and plumbing losses.

Example:

  • 100-gallon fish tank → pump rated 125–150 GPH minimum
  • Add more capacity if your grow beds are elevated or far from the tank

3. Can I use a pond or fountain pump?

Answer: Sometimes, but not always as it will depend on your system.

Many pond/fountain pumps are not designed for:

  • Continuous use
  • Fish-safe materials
  • Handling solids or debris

Stick to pumps labeled as:

  • Hydroponic-safe
  • Aquarium-grade
  • Continuous duty

4. What happens if my pump stops working?

Answer: If your pump fails:

  • Water stops circulating
  • Fish may suffocate from low-oxygen
  • Grow beds may dry out
  • Ammonia can spike and harm fish quickly

Always:

  • Test your pump weekly
  • Keep a backup pump on hand
  • Use a surge protector and GFCI outlet

5. Do I need a timer for my pump?

Answer:Only if you’re using a flood-and-drain system with bell siphons.
Otherwise, most aquaponics pumps should run continuously. Timers are useful in:

  • Media bed systems with manual flood-and-drain cycles
  • Systems where pumps need rest periods for water to drain fully

6. How often should I clean my pump?

Answer:Check and clean the pump every 2–4 weeks, especially in warm climates or systems with:

  • High solids from fish waste
  • Algae growth
  • Leaf debris

Remove the intake cover, rinse out the impeller housing, and scrub off buildup to prevent clogging or overheating.

Conclusion

Choosing the right water pump is one of the most important and most overlooked steps in setting up a healthy, productive aquaponics system. A well-sized, properly installed pump ensures:

  • Steady water flow
  • Consistent nutrient delivery
  • Healthy oxygen levels for fish
  • And peace of mind for you

You’ve just learned what most beginners don’t, how to size, select, and manage a pump that will serve your system for years.

But aquaponics success isn’t just about the equipment, it’s about understanding how the whole ecosystem works together.

Take the Next Step With Expert Support

If you're ready to move from research to results, we invite you to join a 5-hour premium aquaponics video course, trusted by beginners and backyard growers across the world.

Enroll in the Aquaponics Course Now

Your system deserves more than guesswork. Learn it the right way from day one.


 

7 Responses

Francky

Francky

September 06, 2023

Thank you for sharing this informative article on Water Pumps

Mats Wolff

Mats Wolff

May 31, 2022

Its interesting when you said that the air cools the heat created by the pump, which is a major benefit of inline pumps. My uncle owns a farm and wants to hire a water pump repair service since some of his pumps are getting worn out. Thanks for the article and I will forward it to my uncle so that he can repair his pumps as soon as possible! https://www.aemgroup.net.au/water-pumps

Amy Saunders

Amy Saunders

February 08, 2022

Hey there! Now, my neighbor’s grandmother is considering setting up a mall pond in her backyard but she wonders how she can make sure the water stays clear. I like it when you reminded us to get a pump that doesn’t take up too much electrical power. I’ll share this article with her so she’ll be more encouraged to make the right purchase. http://www.betterwaterwells.com

Luke Smith

Luke Smith

February 08, 2022

It was very informative to know that the energy level of a water tank is dependent on its head height. My well has been acting up lately, because it doesn’t produce water as much as it used to. This well is very essential in this neighborhood, so I’ll make sure to inquire for the best well pump services as soon as possible. http://www.downrightdrilling.com/services

Levi Armstrong

Levi Armstrong

July 27, 2021

It’s great that you mentioned that the inline pumps are placed out of the fish tank and are mostly used in larger aquaponics systems. These higher-powered motors are capable of moving larger volumes of water. My brother needs new water pumps to pump clean water into his homemade pond at home. I’ll share this with him to help him find a new one before his fishes in the pond die out. Thanks! https://www.waterworksirrigationandpumpsystems.com/water-pump-repair

Levi Armstrong

Levi Armstrong

July 27, 2021

It’s great that you mentioned that the rule of thumb is that your water pump should circulate the entire water volume in your system at least every two hours. My sister seems to have plumbing problems with her good pipes and isn’t receiving clean water. I’ll share this with her later. Thanks. https://www.russellrobinsonwellman.com/water-well-pump-repair

Levi Armstrong

Levi Armstrong

July 27, 2021

It’s good to know that submersible pumps are cheap, easy to use and install, and do not produce much noise. My dad is looking for a pump for his aquaponics system. He could learn much from this article of yours, so I’ll share this with him tonight. Thanks. https://www.wwpp.co/flint-and-walling-pumps/fandw-commander-s-4-submersible-pumps/

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