Marine ecosystems are not in steady state. They are affected by the environment. Fish populations respond to the variations of environmental factors which vary on spatial and temporal scales. The main aim of this study is to define the effects of atmospheric parameters variability on given fish population such as Atlantic horse mackerel (Trachurus trachurus), pilchard (Sardina pilchardus), Atlantic bonito (Sarda sarda), anchovy (Engraulis encrasicolus), turbot maximos (Scopthalmus maeoticus), blue fish (Pomatomus saltator) in the Black sea, and the Marmara sea and sword fish (Xiphias gladius), gill head sea bream (Sparus aurata), sea bream (Sparus pagrus), chub mackerel (Scomber japonicus), scad (Trachurus mediterraneus) in the Northern part of the Aegean sea. Surface atmospheric parameters such as air temperature, rainfall rate and sea surface temperature values observed in the period between 1980 and 2003 are statistically analysed. Time series analyses show the increasing and decreasing number of populations and aquaculture in different years. In the second part of this study, harmonic analysis techniques were applied. The variations of first-sixth order harmonic amplitudes and phases,provide a useful means of understanding the large and local scale effects on meteorological parameters. The phase angle can be used to determine the time of the year when the maximum or minimum of a given harmonic occurs. Large- and meso-scale effects on fish populations and aquaculture were defined by comparing amplitude and phase values. As a case study, if we compare the population of scad (Trachurus mediterraneus) air temperature with annual total rainfall and annual average air temperature and sea surface temperature, air pressure, it may be concluded that air temperature and rainfall variations play more important role on the population. The results of the study will be evaluated for this pilot project. This study has a key role to define meteorological parameters effects on fish population.