The Real Time Clock (RTC) in the Aquadopp has a resolution of 1 second. The time stamp in the data is taken at the beginning of each measurement. This means that with 1Hz data the middle point in your data point is offset 0.5 second from the reported time. 

When setting the RTC in the Aquadopp, the software sets it to the nearest second when you set it to the PC clock. Hence, the clock may be up to 0.5 second off. This is an offset though, so it is possible to correct for it. To find the offset value you need to use the stop deployment command. Before the actual deployment, start a deployment that you stop directly after. The software will then report the offset between the Aquadopp RTC and the PC clock in milliseconds. You can then use this value to offset your measurement data. 

When you retrieve the instrument, the software will report the time difference again. If you make sure the PC clock to GPS time, you will then see how much the Aquadopp clock has drifted (typical value is 1 second/week). A first order correction of the drift in the Aquadopp would be to distribute the drift evenly throughout the measurement period. Provided that the temperature of the Aquadopp does not change too much during the measurement, the final time scale of you measurement will probably be quite good.