It is very difficult to answer your question as we don't know what model you are using, what data you have and what the specific characteristics of your catchment are.
This list is mainly to resolve technical issues with hydromad. I am not sure that we can solve your hydrological problems.
Low NS values can arise from several directions. It can be due to streamflow data with high variability, it could be due to lack of spatial representation of the rainfall or ET data, it could be due to measurement errors, and it could be because the model just simply struggles to fit the complexity of the data.