Marine ecosystems are not in steady state. They are affected by the environment. Fish populations respond to the variations of environmental factors which varies 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 horse mackerel (Trachurus trachurus), pilchard (Sardina pilchardus), atlantic bonito (Sarda sarda), anchovy (Engraulis encrasicolus), grey mullet (Mugil cephalus), blue fish (Pomatomus saltator) in the Black sea, Marmara sea, and swordfish (Xiphias gladius), gill head sea bream (Sparus aurata), sea bream (Sparus pagrus), chub mackerel (Scomber japonicus) 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, aquaculture, in different years. In the second part of this study, harmonic analysis techniques were applied on data. 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 anchovy (Engraulis encrasicolus) with annual total rainfall rate and annual average air temperature, it is concluded that rainfall variations play more important role on the population. This study has a key role to define the climate changing effects on meteorological parameters.