How to Start a Backyard Aquaponics System from Scratch

When we decided to incorporate aquaponics into our homestead, we made every mistake possible in the first season. Water chemistry swings that killed entire batches of fish. A grow bed that collapsed under the weight of saturated media. A pump failure at 2 AM in January. We're sharing all of it so you don't have to learn the hard way.

This guide covers everything from the first system design sketch to harvesting your first catfish. We'll walk through the grow troughs and raceway setup we eventually landed on, why we chose the species we did, and how we keep everything balanced year-round.

What Is Aquaponics, Actually?

Aquaponics is a closed-loop system that combines fish farming (aquaculture) with soil-less plant growing (hydroponics). Fish produce waste. That waste is broken down by beneficial bacteria into nitrates. Plants absorb those nitrates as nutrients. The cleaned water returns to the fish. Nothing is wasted.

On our homestead, we've scaled this across three system types: raised grow troughs for leafy greens and herbs, long raceways for grow-out fish production, and our natural pond ecosystem for crawfish and larger catfish. Each system has different management requirements — and different rewards.

System Types: Which One Is Right for You?

Media Bed (Best for Beginners)

A media bed is a grow container filled with porous media (expanded clay pebbles, lava rock, or river gravel) where both plants grow and beneficial bacteria colonize. Fish water floods and drains cyclically. This is the most forgiving system type and where most homesteaders should start.

Deep Water Culture (DWC) / Raft Systems

Plants float on foam rafts over a shallow channel of fish water. Highly productive for leafy greens at scale. Requires more precise water management but supports higher fish density than media beds.

Raceways (What We Use for Production)

Long, narrow channels — similar to trout raceways — where fish are grown out at higher densities with continuous water flow. We run ours at 4 feet wide, 2 feet deep, and 20 feet long for catfish and tilapia production. Separate grow troughs off the raceway handle our vegetable production.

Natural Pond Integration

Our natural pond handles crawfish and larger catfish in a semi-managed environment. We stock, manage water quality with aeration, and harvest seasonally. This is the lowest input but also lowest control system — perfect for crawfish which thrive in natural conditions.

Species Selection: What We Raise and Why

Start with tilapia. They tolerate water quality swings, grow fast, and are forgiving of beginner mistakes. Once you have a stable system and understand your chemistry, add catfish. Crawfish can go into your pond from day one. Save freshwater prawn and flounder for when you have experience under your belt.

Sizing Your System

The most common beginner mistake is going too small. A 100-gallon tank feels large until you realize how many fish you can actually grow in it. Here are the ratios we work with:

• Stocking density: 1 lb of fish per 5–10 gallons of water (start at 10, move toward 5 as you gain confidence)
• Grow bed ratio: 1:1 to 2:1 grow bed volume to fish tank volume
• Raceway flow rate: Complete water volume exchange every 1–2 hours
• Pond aeration: 1 HP aerator per 1–2 acres of pond surface

The Nitrogen Cycle: Don't Skip This

Before you add a single fish, your system needs to cycle. This means establishing colonies of two bacteria types: Nitrosomonas (convert ammonia to nitrite) and Nitrobacter (convert nitrite to nitrate). Without them, ammonia builds up and kills your fish within days.

Cycling takes 4–6 weeks. You can speed this up by:

1. Adding a small amount of fish food daily to produce ammonia as a bacteria food source
2. Using bacteria starter culture from an established aquaponic or aquarium system
3. Maintaining water temp between 77–86°F to accelerate bacterial growth
4. Testing daily — you want ammonia and nitrite at zero before stocking fish

What to Plant in Your Grow Beds

Start with plants that love high nitrogen — they'll consume fish waste fastest and keep your water clean. Our top performers in the grow troughs:

• Leafy greens: Swiss chard, kale, lettuce, arugula, spinach — fast growing, heavy feeders
• Herbs: Basil, mint, chives, parsley — incredibly productive in aquaponics
• Fruiting plants: Tomatoes, peppers, cucumbers — require more mature, stable systems
• Avoid: Root vegetables (carrots, potatoes) — they need soil, not water

Harvesting Fish: Our Approach

We harvest our tilapia and catfish with a combination of seine nets in the raceways and hook-and-line in the pond. Fish go immediately into ice slurry, then to our processing station. From tank to cold storage in under 30 minutes.

Crawfish are harvested with wire mesh traps baited with fish scraps or chicken carcasses. We empty traps in the early morning and get about two harvests per week during peak season (April through June in our climate).

Real Cost Breakdown: Our First System

Our expanded raceway system cost significantly more — but the first system paid for itself within 18 months in fish, plants, and reduced grocery bills.

Mistakes We Made (So You Don't Have To)

1. Not cycling the system first. We added fish too early and lost an entire batch to ammonia poisoning.
2. Underpowered aeration. Fish need a lot of dissolved oxygen. We doubled our air pumps after our first summer.
3. No backup power. A pump failure during a cold snap killed fish. We now have a generator on standby.
4. Wrong grow media. Gravel compacted and killed the flood-drain cycle. Switched to expanded clay and never looked back.
5. Overstocking too fast. Patience with stocking density is the single most important thing. The system needs time to mature.

Aquaponics is one of the most rewarding systems on a homestead — but it requires real attention, especially in the first year. The payoff is exceptional: year-round fish protein, an insane amount of vegetable production, and a system that gets better every season as the biology matures. We wouldn't trade it for anything.