Microalgae are widely exploited for numerous biotechnology applications, including biofuels. In this context, Chlamydomonas debaryana and Chlorococcum sp. were isolated from Fez freshwater (Morocco), and their growth and lipid and carbohydrate production were assessed at different concentrations of NaCl, NaNO3, and K2HPO4. The results indicate a small positive variation in growth parameters linked to nutrient enrichment, with no considerable variation in carbohydrate and lipid levels in both algae. Moreover, a negative variation was recorded at increased salinity and nutrient limitation, accompanied by lipid and carbohydrate accumulation. Chlorococcum sp. showed better adaptation to salt stress below 200 mM NaCl. Furthermore, its growth and biomass productivity were strongly reduced by nitrogen depletion, and its lipid production reached 47.64% DW at 3.52 mM NaNO3. As for Chlamydomonas debaryana, a substantial reduction in growth was induced by nutrient depletion, a maximal carbohydrate level was produced at less than 8.82 mM NaNO3 (40.59% DW). The effect of phosphorus was less significant. However, a concentration of 0.115 mM K2HPO4 increased lipid and carbohydrate content without compromising biomass productivity. The results suggest that growing the two Chlorophyceae under these conditions seems interesting for biofuel production, but the loss of biomass requires a more efficient strategy to maximize lipid and carbohydrate accumulation without loss of productivity.