My answer comes from an underwater acoustics perspective which means dB scaling is used throughout to make the arithmetic easier.
The transducer kit comes with a calibration printout for the actual hydrophone as shown below. If your hydrophone didn't come with this, you'll need to consult the specification sheet and use the typical sensitivity which makes the experiment questionable.
Calibration sheet from an actual B&K 8103 transducer.
Hydrophone Sensitivity
From the graph, find the Open Circuit Voltage (OCV) sensitivity.
In the above example chart the base sensitivity is -211.5 dB//1V/uPa as shown in the upper red boxed area.
At 60 kHz, the sensitivity is -211.5 - 2.0 = -213.5 dB//1V/uPa.
Thus, at 60 kHz the OCV = -213.5 dB//1V/uPa.
Receive Level
To find the Sound Pressure Level (SPL) at the hydrophone:
\$ SPL = (Vout_{dB} - G) + OCV \;\;\$ in dB//1µPa
Where:
\$ Vout_{dB} \$ = measured rms output voltage of the amplifier in dBV
\$ G \$ = gain of amplifier in dB
Floobydust
In the following comments, I refer to doing computations using oscilloscope maths functions. If you use a math tool such as R, the comments are still valid, i.e., know how the tool functions.
A continuous (CW) signal is not recommended for acoustic measurements unless you have a very large free-field test range.
Acoustic measurements are generally done using burst signals so reflections don't corrupt the measurement. This means using a FFT may not be a good choice since there will be limited cycles to perform the FFT maths. You may be better off using a time windowed Vrms voltage reading that encompasses a number of complete cycles. Averaging is highly desirable since this reduces noise and gives better bit-depth (dependent on the complexity of the oscilloscope). Be sure to trigger the oscilloscope on the transmit burst.
Set the burst rate (number of transmit pings per second) so tank reverberation does not influence the measurements from previous bursts reverberation. 10 bursts per second is a good starting point.
To determine what pulse length you should use, perhaps use a 100 cycle burst at the desired frequency and monitor the received signal. At some time, the signal will become corrupt due to constructive/destructive interference from reverberation. Set the number of cycles of the burst so the received signal isn't corrupt. You state that the hydrophone is near the surface which means you get corruption from the surface bounce. Same goes for the projector which will send energy bouncing off of various surfaces. You can also test for surface bounce issues by causing ripples on the water surface. If the signal changes with surface ripples, you have surface interference which is undesirable. It is best if you can locate the projector and hydrophone at least 1 metre from any surfaces, especially at the frequencies you are considering.
If you are going to use the FFT function, use flattop windowing. This gives the most accurate amplitude reading of the various common window types due to low ripple and wide bandwidth.
Be sure the FFT gives a rms reading. Some oscilloscope don't.
Be sure the signal covers the whole screen width. FFTs on better oscilloscopes will compute the FFT on the displayed signal.
When using bursts, be sure that you're getting the right amplitude results. Certain oscilloscopes, like inexpensive Rigol scopes, give wrong amplitude results for delayed burst signals.
As previously mentioned, you need lots of cycles for FFTs. Burst signals in small water tanks generally do not have enough cycles to compute a good FFT which is why I recommend using the oscilloscope's Vrms measurement function.
Be sure you measure the gain of the amplifier over the frequency span of interest. The frequency response of the amplifier may be different at different gain settings. Heed the old adage: Know your test equipment!
If you add cable to the existing hydrophone cable, this may affect the sensitivity. The additional cable will act as a capacitive load on a complex impedance which creates a voltage divider and reduces the sensitivity. The simple hydrophone output capacitance is around 3.7 nF (see the lower red box in the example chart) which means a couple metres of cable probably won't affect the sensitivity much. To be sure, you need to perform a measurement with and without the additional cable.
The input impedance of the amplifier should be high impedance, > 100k ohms for your frequency range of 20 kHz to 60 kHz (or did you mean 20 Hz to 60 kHz?).
Also check that the amplifier input capacitance won't affect the measurements. I would suspect that anything under 100 pF should be OK. Again, test.