How to Set Up Your 40oz Micro Reef Tank

PNW Custom
5 days ago
4 min read

This guide will walk you through the full setup process: from unboxing to plugging everything in and preparing your reef for its first inhabitants. Whether you’re brand new to reefing or a seasoned hobbyist looking for a clean, compact desktop setup, this walkthrough will help you get your tank up and running smoothly.

🎥 Watch the Full Setup Video

❗NOTE: This video includes additional accessories such as the Auto Top Off, Heater, Temperature Probe, and Microscape that do not come in the standard version of the Micro Reef Kit. These items are optional and not necessary for set up.

Follow along step-by-step in the video above as we unbox, assemble, and start up the 40oz Micro Reef (Full Setup). Below, you’ll find a written summary and time-stamped breakdown of everything we covered.

What’s in the Box

Your PNW Custom 40oz Micro Reef includes everything you need to get started:

Display Tank + Stand
3‑Compartment Sump Filtration
Dual‑Drain Return
Adjustable 3W, 50 GPH Return Pump
5W Switchable LED
Polycarbonate Display & Sump Lids
Black Drain & Return Nozzles
Integrated Water‑Level Indicator
Filter Floss & Bio Media

If you have the Full Setup, you'll also see these accessories in your box:

Some additional accessories (as seen in the video):

Setup Steps

1. Unboxing & Overview (0:00 – 3:40)

Start by removing your tank and all included accessories from the packaging.
Inspect each item to make sure everything arrived safely.
Remove the wrapping from both lids.

2. Installing the Light (3:40 – 4:35)

Unbox the light, power supply, and instruction manual.
Remove the screw from the bag and install it into the light display.
Slide the light onto the bracket on the back of the tank and screw in place.
Move the light arm out of the way for now.

3. Setting Up the Sump (4:35 – 6:12)

Remove the display tank and set to the side.
Remove the sump.
Pull the wire out and put it through the back of the sump cut out so it is out of the way.
Add a small amount of filter floss to the first compartment in the sump.
Add the bio media into the middle compartment (no need to arrange it in any particular way).
Slide the sump back into the frame and add the sump lid.
This setup provides mechanical, chemical, and biological filtration, helping maintain stable, crystal-clear water in your micro reef.

4. Adding Live Sand & Rock (6:12 – 6:53)

Slide the display onto the frame and hook up the nozzle. The nozzle slides onto the silicone tube and locks into place.
Pour the bag of live sand into the display.
Spread out the sand so that it creates an even layer. Remove any excess sand (if desired).
Remove the rockscape from the towel. This was keeping it wet during transit.

5. Filling the Tank (6:53 – 7:39)

Add the drip tray under the tank to control any spills.
Slowly fill the tank with saltwater until it is about 70% full.

6. Installing the Heater (7:39 – 8:27)

Remove the heater from the box.
Add the heater to the sump (right in front of the pump).

7. Adding the Auto Top-Off System (8:27 – 12:46)

The ATO includes the power supply, sensor, pump, tubing, check valve, clamp/clip, and a user manual.
Start with the sensor. It's magnetic and it will sit right above the side of the pump. Push it through the back of the sump and put it above the pump. Make sure it stays vertical.
Hook up the power supply and pump on the other side by using the included tubing.
Remove the ATO container lid.
Make sure the check valve arrow is pointing up.
Install the check valve onto the bottom of the tube and push it into place in the top of the container.
Plug into the power supply.
Measure how much tubing will be needed and cut it to size.
Screw the clamp together and add the included screw.
Tighten it down into the notch on the back of the sump.
Run the tube through the clip.

8. Cord Management & Organization (12:46 – 14:30)

Bundle cords neatly and route them behind the tank for a clean, professional appearance.
Velcro straps or cable clips work great here.
A tidy setup not only looks better but also makes maintenance easier.

9. Final Water Level & Startup (14:30 – 15:59)

Slowly fill the tank to the water level line and ensure the auto top off sensor is working correctly.
Add water to the ATO container.

After Setup: Beginning the Cycle

Cycling is the process of establishing beneficial bacteria that convert toxic ammonia into less harmful nitrate.

Dry Rock, Dry Sand, and Dry Media: This cycle will take the longest because there’s no existing bacteria to start with. You’ll rely on natural bacteria colonizing over several weeks.
Dry Rock, Live Sand, and Dry Media: The live sand introduces a small bacterial population that helps jump-start the process, slightly reducing the cycling time.
Live Rock, Live Sand, and Live Media: This provides the fastest and most stable start, as all three components are already full of beneficial bacteria that instantly begin processing waste.

Since micro tanks are small and sensitive, it’s best to avoid chemical additives and instead let the cycle establish naturally, testing water parameters and waiting until ammonia and nitrite reach zero before adding livestock.

Pro Tips

Top off with fresh RODI water (not saltwater) when doing manual top-offs.
Wipe the lids regularly to prevent salt creep.
Always unplug electronics before performing maintenance.
Download and print our FREE Maintenance checklist to stay on top of weekly maintenance.
Reference our fish and invertebrate compatibility guides to see what types of fish are suitable inhabitants for the 40oz Micro Reef. There are multiple small gobies (under 2 inches) without a swim bladder that are great options.

Join the Micro Reef Community

We love seeing how you personalize your Micro Reef! Tag @pnwcustom on Instagram or TikTok to share your setup, and we may feature your tank on our page.

Explore accessories, frag racks, and coral packs designed specifically for desktop tanks on our website.

Welcome to the PNW Custom family and happy reefing!