How I Set Up Automatic Water Changes on My Reef Tank Using Neptune DOS

After 5 years of running continuous automatic water changes, I'm sharing my setup using Neptune Systems DOS. Forget the standard task-based approach—this method is more reliable and has been running strong with zero issues.

One of the best decisions I made for my reef tank was automating water changes. Manual water changes are tedious, easy to skip, and let's be honest—life gets busy. My Neptune DOS has been running automatic water changes continuously for over 5 years now, and I haven't looked back.

I'm a full Neptune Apex power user with 40+ modules controlling my system, but today I'm focusing specifically on the auto water change setup. This approach is slightly different from the standard Neptune task-based method, and it's based on one of the best tutorials ever written for Apex programming.

Credit Where It's Due: SuncrestReef's Legacy

Before diving in, I have to acknowledge SuncrestReef from the Reef2Reef community. His Neptune Apex tutorial series is legendary in the reefing world—comprehensive, well-documented, and written by someone who truly understood both IT systems and reef keeping. Unfortunately, he's since retired from contributing, but his tutorials remain the gold standard for Apex programming.

His Part 9 DOS tutorial is what shaped my entire approach to automatic water changes. If you want the deep technical dive, I highly recommend checking out his full tutorial series.

What is the Neptune DOS?

The DOS (Dosing and Fluid Metering System) is Neptune's dual-head peristaltic pump designed for the Apex controller. Each head operates independently with six speed settings and can run forward or reverse. It can pump vertically up to 24 feet and practically unlimited horizontal distances—perfect for basement equipment rooms or remote setups.

While most people use the DOS for dosing additives like alkalinity and calcium, it's equally capable of handling automatic water changes—which is exactly what I use it for.

My Auto Water Change Setup

neptune-apex-system-auto-water-change-system-dos-setup

Here's what I'm running:

Close to 2 gallons per day of continuous water exchange
Approximately 10% water change per week
Running 24/7 in continuous mode
5+ years of reliable operation with no issues

The beauty of continuous water changes is that the water level never fluctuates significantly. The DOS adds fresh saltwater while simultaneously removing old tank water. No need to disable your ATO, no skimmer going crazy from water level changes, no return pump running dry.

Why This Approach is Different (And Better)

Neptune provides a built-in "DOS Automatic Water Changes" task in Fusion that most people use. It works, but there's an issue: the task programs the drain pump to run counterclockwise (reverse direction).

Here's why that's a problem: when you need to calibrate your DOS or prime the lines, both functions require the pump to rotate clockwise. With Neptune's default setup, you'd have to disconnect and reconnect your tubing every time you calibrate or prime. That's annoying.

The Better Way

Instead of following Neptune's default tubing diagram, reverse the tube connections on your drain pump. Then change the programming from "Remove" to "Add" mode. Think of it as "adding water to the drain" instead of "removing water from the tank."

The result? Both pumps rotate clockwise during operation, and you can calibrate and prime without touching your tubing. This is exactly how SuncrestReef recommended doing it, and it's been flawless for me.

Step-by-Step Setup

1. Hardware Setup

You'll need:

Neptune DOS unit connected to your Apex
Fresh saltwater reservoir (I use a 40-gallon Brute trash can)
Drain container or direct drain connection
Enough tubing to reach your reservoirs

2. Tubing Configuration (The Key Difference)

Left pump (new saltwater): Connect normally following the arrows on the pump head. Input from your saltwater reservoir, output to your tank/sump.

Right pump (drain): Connect the tubes REVERSED from the arrows. Input from your tank/sump, output to your drain or waste container.

3. Apex Programming

Run the DOS AWC Setup task in Fusion to create the initial configuration. Then make this one critical change:

Go to the drain pump's schedule and change the interval from "Remove" to "Add". This is the secret sauce. It tells the pump to rotate clockwise while still functionally draining water because you've reversed the tubing.

4. Calibration

Use the included graduated cylinder to calibrate both pumps. The DOS will dispense approximately 40mL, you measure what actually came out, and enter that value. The system compensates automatically. Recalibrate whenever you change tubing or pump heads.

5. Priming

Hold the priming button or set the output to manual ON until liquid fills the entire tube length. Watch for air bubbles—if you see any, your connections aren't airtight. Pro tip: heat the tubing ends with near-boiling water before connecting to get a perfect seal.

Why Continuous Water Changes Work So Well

There's a great explanation from a 2005 ReefKeeping article that still holds up:

"A continuous water change of 30% exactly matches one batch 26% water change. As with very small batch water changes, these have the advantage of neither stressing the organisms (assuming the change is done reasonably slowly), nor altering the water level in the aquarium."

Yes, you technically "waste" a tiny bit of new saltwater compared to doing a batch change (draining first, then refilling). But the benefits massively outweigh this:

Water level stays constant
No need to disable ATO or skimmer
No float or optical sensors required
Parameters stay more stable (no weekly swings)
Less stress on livestock
Set it and forget it

Maintenance and Longevity

The DOS pump heads are user-replaceable and surprisingly durable. I proactively swap mine yearly for the AWC unit, but honestly, I haven't seen significant wear even after continuous 24/7 operation. They could probably last much longer.

One thing to watch: after about 4 years, my new saltwater tubing developed sediment buildup. Calibration started drifting way off. The fix was simple—circulate citric acid through the tubing to dissolve the deposits. Worked perfectly.

Pro Tips: Using the Advanced Tab

The Advanced tab in your DOS output settings lets you add conditions to pause water changes. Here are some useful ones:

Pause during maintenance:

If Output Maintenance = ON Then OFF

Pause during feed cycle:

If FeedA 005 Then OFF

Pause if pH is too high:

If pH > 8.40 Then OFF

Never use "Set ON" or "Then ON" in the Advanced tab—it will override your schedule and pump continuously at 25mL/min, potentially flooding your tank or draining it completely.

Five Years Later: The Results

My tank has never been more stable. Parameters barely fluctuate week to week. I top up my saltwater reservoir maybe once every two weeks, and that's the extent of my "water change" labor.

The continuous small exchanges keep nutrients from building up, export waste consistently, and replenish trace elements steadily. It's one of those "why didn't I do this sooner" upgrades.

Final Thoughts

If you're running a Neptune Apex and haven't automated your water changes yet, the DOS is worth every penny. The key is setting it up correctly from the start—reverse those drain tubes, change to "Add" mode, and never worry about reconfiguring for calibration again.

Thanks again to SuncrestReef for the foundational knowledge. His retirement from the community was a loss, but his tutorials continue to help reefers worldwide—including me.

Happy reefing! 🐠🪸