You are mixing your metering. There are potentially two types of metering going on. The first is your ambient light metering. This is your spot, center, evaluative (matrix in Nikonese). In your example, this would be your background exposure, i.e. whatever your meter says when you point it at something. It isn't clear in your example what setting was on your camera when you got the f4, 1/90 at ISO400. Did you spot the water or is it center weighted?
Now, assuming you are using TTL flash. There is a second metering going on that tells the flash how long to flash. How your camera does this is a big dark proprietary secret, but it is different and not necessarily related at all to your ambient light metering choice.
I am willing to guess that in your example, with TTL flash, you will overexpose the turtle, regardless of your metering choice. The flash doesn't know that only the turtle needs a "little" flash. It doesn't know it can lighten anything past about 5 ft. away, but it doesn't mind trying.
Here's the old film technique:
1) Set meter to spot. Camera on manual mode. Aim at blue water that I want to be neutral luminosity. Set exposure.
2) Strobes set to manual. Set strobe power based on Guide number/estimated distance to foreground subject. Bracket.
3) Pray on the way to the lab to pick up slides.
New digital technigue:
1) Set meter to matrix. Camera on manual mode. Set exposure at roughly what the meter says, maybe underexpose.
2) Set strobes to half power.
3) Shoot. Look at image/histogram.
4) Change f/stop for background exposure adjustment. Change strobe power for foreground exposure adjustment.
TTL Flash (I don't want to mess with 'nuttin)
1) Set to matrix meter.
2) Set exposure comp to between -.5 and -2.0
3) Fire away.
4) Adjust exposure comp if using digital.