Unfortunately HOMER can model only one hydro system

If your system comprises multiple hydro systems, then to model that system in HOMER you will have to combine them into an equivalent single hydro system.  Doing so will require a lot of preprocessing.

One possibility would be to calculate the power output of each hydro turbine in each time step of the year, and sum that to calculate the total hydro power output in each time step.  Then you could import that into HOMER as stream flow data, and adjust the hydro turbine inputs to result in a 1:1 ratio of power output to stream flow.  In other words, you would adjust the hydro turbine properties to ensure that in a time step wherein you specify a 'stream flow' of 1 L/s, the hydro turbine produces 1 kW.

If you did that, then the hydro turbine in HOMER's schematic diagram would represent all three of your hydro subsystems, and its output would equal the combined output of the three real hydro turbines.