Marine microbes are an essential component of food web in every ecosystem. These microbial communities are straddling in broad range of size spectrum, and can be categorized as pico-, nano- and microplankton. They are key players for the sustenance of food web as re-mineralizers, grazers, and ultimately prey for higher trophic levels. Marine microbes occupy a wide range of habitats from pelagic to benthic and estuarine to coastal waters. However, rapid urbanization in coastal cities may induce the pollution and possibly, altered the microbial diversity. Therefore, it is imperative to study planktonic microbial community and their role in in marine ecosystem health, which is understudied in Pakistan waters. In this investigation, firstly an in introduction to marine ecosystem with emphasis on role of microbes their importance in general and information about coastal waters of Pakistan, the study sites and research objectives are presented in chapter 1. The chapter 2 was compiled together the already published research work on microplankton community conducted in waters along the coast of Pakistan (northern Arabian Sea). This comprehensive checklist is the updated version the previous checklist. In chapter 3, planktonic microbial community inhabiting the Manora channel, coastal waters of Karachi was investigated on spatio-temporal scale with their response to hydrographical conditions. The community categorized in pico-, nano- and microplankton was assessed qualitatively and quantitatively that revealed marked seasonal variation with high cell densities in summer southwest (SW) monsoon season. It was clearly evident that community composition did not vary substantially between the stations, but was almost high in abundance at St-A as compared to St-B, in particular with higher values of cell abundances, Chl a, POC and PON with lower values of DO observed at St-A indicating the influence of organic and inorganic pollution fluxed through Lyari river, reflected eutrophic condition. Chapter 4 presented further detailed contribution of nanoplankton (NAN) community composition. The nanoplankton were primarily grouped into phototrophic (PNAN) and heterotrophic (HNAN) fraction according to their trophic status. The nanoplankton communities in PNAN were consist of three groups namely nanoflagellates, diatom and dinoflagellates, whereas, heterotrophic group was constituted with nanoflagellates and dinoflagellates only. The seasonal distribution and abundance on annual cycle exhibited a typical pattern consisting of high values in summer month and PNANs were the most significant fraction, contributed about 85% and 80% to total NANs abundance at St-A and St-B respectively and positively correlated with chlorophyll-a. The focus of study in Chapter 5 was to assess the micropankton community (diatoms, dinoflagellates and ciliates) from comparatively clearer waters (off the Hub delta), Karachi in the northern Arabian Sea, Pakistan. Presence of bloom forming diatoms Cylindrotheca closterium and toxic Pseudo-nitzchiac f. pungens as the most abundant species with a red tide ciliate Mesodinium rubrum during the study suggested the long term assessment of toxic microplankton population (species) and their influence on human health. In situ incubation experiment was also conducted to assess the growth rate of ciliate community using the fractionation method during winter season in the Manora channel waters, Karachi coast (Chapter 6). A total of twenty nine ciliate taxa were observed in the unfractionated (control) and fractionated (150µ) and (10 µ) samples. The mean in situ growth rate of the total ciliate population was ranging from 0.28 to 3.43 d-1.Over all, the growth rate was lowest in the un-fractionated samples and high values were recorded for both size fractions with highest in Fr<10 µm. The loricate ciliate was found with high growth rate of 1.86 d-1 in unfractionated, 2.65 d-1 in Fr<150 µm and 3.43 d-1 in Fr<10 µm sample. The present study clearly revealed that predation seems to play a major role and may restrict the growth rate. This research is the first of its kind which contributes valuable information on pico-, nano- and microplankton community structure and their growth and grazing impact in the ecosystem. It is a prerequisite to envisage the environmental change which may influence the microbes and their role in essential processes by bridging the gap in research for future perspective.