And my English might be a little bit of a problem!
OK. I'll stop picking on your question vs. statement issues.
I've got a 3D printed paddle wheel, cased in a body that lets the water pass trough, and when the water goes trough, it spins the paddle wheel right?
OK.
I've measured the pulses, and it's roughly around ~16Hz
Using the Arduino? How is the sensor connected to the Arduino? What does the code look like?
If you ARE reading data using the Arduino, then you can know that the state of the sensor changes, and when that happened. So, put the code to read the sensor, and record when the state change (to magnet no longer here or to magnet just arrived, but not both) happens (using millis()).
Then, call that function from loop(). Independently, check the current time (using millis()), and compare the current time to the last state change time (that the function recorded). If the last state change detection time is too old, sound the alarm.