A first study on nitrogen to phosphorus (N:P) supply ratio with different N sources (NaNO3, urea, and L-Asparagine) and salinity within the cultivation medium of microalgal species towards biomass and lipid enhancement is demonstrated. Among the three nitrogen sources, L-Asparagine at N:P supply ratio of 75:1 and 100:1 gave the highest biomass concentration for the tested microalgal species. For chlorella sp. NITT 02, the DCW of 1.257 ± 0.003 g L−1 at N:P = 100:1 and 1.256 ± 0.005 g L−1 at N:P = 75:1 was obtained for L-Asaparagine, followed by urea (N:P = 100:1 → 0.842 ± 0.002 g L−1; N:P = 75:1 → 0.843 ± 0.004 g L−1). The DCW of Picochlorum sp. NITT 04 with L-Asparagine (N:P = 100:1 → 0.964 ± 0.026 g L−1; N:P = 75:1 → 0.965 ± 0.034 g L−1) and urea (N:P = 100:1 → 0.911 ± 0.012 g L−1; N:P = 75:1 → 0.908 ± 0.01 g L−1) was attained maximum than NaNO3. The systematic exploration of the interaction between N:P ratio and salinity towards lipid content enhancement were performed by RSM-CCD approach. The optimal N:P ratio of 1.4:0.6 and salinity of 7.5 ppt resulted in maximum lipid content of 49.252 ± 0.187 % for Chlorella sp. NITT 02 with the total FAME content of 93.49 %. For Picochlorum sp. NITT 04, the optimal N:P ratio of 1.4:0.6 and salinity of 24 ppt resulted in maximum lipid content of 49.717 ± 0.073 % with the total FAME content of 91.71 %. The FAME analysis confirms the use of tested microalgal species towards biodiesel production and concurrent use of residual biomass for biorefinery applications.