Hayward AquaRite S3 Troubleshooting Guide: Warnings and Output Problems
The Hayward AquaRite S3 is a salt chlorinator and basic automation controller in one box. It can generate chlorine from dissolved salt and control a variable speed pump, a heater, and even a pool cover, depending on how you wire it.
This guide is written for working pool techs and serious DIY owners standing at the pad with the door open. It focuses on the S3 behavior you actually see day to day: salinity readings, output percentage, warnings, pump control, and cell maintenance.
Quick Reference: Key Readings and Symptoms
Display Dark / No Power
Meaning: No incoming power to the control or internal protection issue.
Next step: Check breaker, wiring, and internal components.
View detailed guide →Not Generating Chlorine
Meaning: Display on but output stays at 0% and pool has no free chlorine.
Next step: Check setpoint, schedule, salinity, temperature limits, and cell condition.
View detailed guide →Low Salt Warning
Meaning: Average salinity below configured low salt alarm value (default ~2700 ppm).
Next step: Verify salt with independent test, add salt slowly, and monitor average reading.
View detailed guide →High Salt Warning
Meaning: Salinity above high salt alarm level (default ~3400 ppm, can be set up to 8000 ppm).
Next step: Compare display to independent test and decide whether to dilute or suspect reading issue.
View detailed guide →Salt Reading Wrong
Meaning: Instant and average readings disagree with drop test or strip.
Next step: Reset averages, clean cell, verify cell temperature is stable.
View detailed guide →Flow / Circulation Problems
Meaning: Pump running but S3 refuses to generate.
Next step: Check flow switch orientation, valve positions, and schedule logic.
View detailed guide →Cold/Hot Water Shutdown
Meaning: Cell temperature outside allowed band (roughly 50-140°F).
Next step: Verify temperature on display and decide if generation is needed in cold weather.
View detailed guide →TurboCell Scaling
Meaning: Output dropping over time, heavy white scale visible in cell.
Next step: Pull and inspect cell, acid wash if needed, test water balance.
View detailed guide →Pump Schedule Not Working
Meaning: S3 supposed to control pump but schedules, speeds, or modes misbehave.
Next step: Check RS-485 wiring, Smart Relay connections, and control mode settings.
View detailed guide →How the AquaRite S3 Works (Quick Overview)
At a high level the S3 is doing four jobs simultaneously:
1. Read sensors and system state
- Flow switch in the return line
- TurboCell current, voltage, and internal temperature
- Optional water and air temperature sensors
- Optional pool cover switch input
2. Decide when chlorine generation is allowed
The unit will only generate when:
- It sees adequate flow through the cell
- The pump is running according to its own schedule or an external timer
- Salt level is within its allowed band (roughly 1200-8000 ppm, target 3200 ppm)
- Temperature at the cell is in range (derates in the 50s°F, shuts down below ~50°F or above ~140°F)
3. Drive outputs
- Apply DC power to the TurboCell, reversing polarity periodically to shed scale
- Control a Hayward VSP directly over RS-485 or a single-speed pump through a Smart Relay
- Switch a heater's low voltage remote contacts when heat is called and a water sensor is installed
4. Expose status and configuration
The front panel shows:
- Chlorination percentage
- Average and instant salt levels
- Cell temperature
- Pump and heater states
- Warnings when salinity, temperature, or other parameters are outside configured limits
Most Common Problems
1. AquaRite S3 Dead or Screen Blank
- No line voltage at the feed, tripped breaker, or switched leg off
- Miswired 115 or 230 volt input harness
- Internal fuse or board damage from a surge or incorrect wiring
2. Display On But No Chlorine in Pool
- Chlorination disabled in menu or setpoint too low for current pump runtime
- Pump schedule does not overlap when you expect chlorine production
- Salinity out of band and unit has derated or shut down
- Cell is scaled up or near end of life
3. Low Salt Warning
- Real dilution from backwashing, drain and refill, or heavy splash out
- Salt level never brought up to at least lower end of operating band (~1200 ppm minimum)
- Cold water dropping the cell's conductivity and reading
- Early signs of a tired cell
4. High Salt Warning
- Too much salt added in one shot without testing
- Small pools where a "just add one bag" habit overshoots quickly
- Retrofit on an old pool that already had significant salt from years of chlorination
5. Salt Reading Wrong or Unstable
- Average salt has not yet caught up to a recent change
- Cell scaled or partially blocked, altering conductivity
- Cell temperature very different from bulk pool water
- Testing errors with strips or an old drop kit
6. Flow or Circulation Problems
- Flow switch installed in wrong orientation or too close to an elbow
- Valves set so water bypasses the cell
- Pump on external timer while S3 expects to control it
7. Temperature Related Shutdown and Freeze Protection
- Cell temperature below its allowed band
- Air sensor and freeze protection enabled
- Heater plumbing sending very hot water straight into the cell
8. TurboCell Scaling, Cleaning, and End of Life
- High calcium or high saturation index problem
- Cell plates choking on scale and need proper cleaning
- Cell aged and near end of designed lifespan
9. Pump Control and Scheduling Issues
- RS-485 wiring or Smart Relay wiring incorrect
- Control mode configuration wrong (external vs internal control)
- Pump firmware or compatibility issues
Basic Diagnostic Checklist
Verify safe power: Confirm breaker is on and the AquaRite S3 is receiving proper voltage. Check that the display is lit.
Confirm flow and hydraulics: Pump on, filter pressure reasonable, valves open to the pool. Flow switch installed with arrow pointing in direction of flow.
Check display readings: Note chlorination percentage, average and instant salt levels, cell temperature, and any warning messages.
Review schedule settings: Verify pump schedules are set correctly and match when you expect the system to run.
Water chemistry sanity check: Salt, pH, alkalinity, and calcium hardness roughly in recommended ranges. If balance is badly off, correct that before blaming equipment.
Visual inspection: Look for obvious corrosion, overheated terminals, rodent damage in the box, and visible scale or debris in the cell.
When To Call A Professional
Stop and involve a qualified pro when:
- You need to open or rewire the incoming power feed or work inside the house panel
- Internal fuses have blown more than once or blow again immediately after replacement
- The board shows visible burn marks, bulged components, or melted traces
- You are not comfortable handling muriatic acid for cell cleaning or adjusting water chemistry
- The system is under warranty and you suspect a board or cell failure
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