The study attempted to characterize the physicochemical limnology and the algal community of El-Timsah Lake during March 2004 to May 2005. The physicochemical limnology plays a key role in the blooming characteristic of benthic mats during spring season. Two mats were recognized visually of green and black colours. The green mat was constructed by the mechanical entanglement of filaments of Cladophora with four species of diatoms trapped within the filaments. In addition, the mat also bears fragments of Ulva, Enteromorpha and Chaetomorpha. The black mat was constructed primarily from filaments of Oscillatoria nigroviridis with two genera of coccoid cyanobacteria and some diatom species. Mat-forming algae grow initially on the bottom, but often “breaks away" to create numerous floating pads on the surface of the lake. Although, marine macroscopic algae were identified during this investigation, a brackish stratification was consistently confirmed by the appearance of some indicators of brackish type of diatoms such as Melosira nummuloids, Achnanthes brevipes var. intermedia, Skeletonema subsalsum, Navicula capitata, Navicula digitoradiata and Surirella brebissonii.