The independent variable is the variable that is changed or controlled in the experiment. The dependent variable is the variable that you are testing. The dependent variable is “dependent” on the independent variable. As you change the independent variable, the effect on the dependent variable is observed and recorded.
So, in your experiment, the pH is your independent variable as is the amount of substrate. As you change these (separately), everything else being the same (e.g. temperature), your product formation changes...so the product formation is the dependent variable.
The temperature could also be considered as an independent variable...as you are controlling it (no change). I would say 3 independent variables (pH, substrate amount, and temperature). Variable is only 1 (product formation).