The spatial and temporal distribution of 5 abundant ciliate species and of ciliate diversity in a Mexican coastal lagoon were studied. The goals were to: examine small scale (<100 m) and large scale (1 to 10 km) patches; indicate how different classical and geostatistical techniques can be used to examine these patches; make inferences concerning ciliate distribution, behaviour, and diversity in the lagoon; and compare the performance of 4 geostatistical methods for modelling ciliate abundance and diversity distributions. Ciliates were sampled at 10 sites, distributed around the lagoon to estimate lagoonal scale patches and at one grid, in the centre of the lagoon, to assess sub-lagoonal patches (1 to 200 m); samples were taken at these sites at 5 times through a year, covering the rainy and dry seasons. Samples were also taken weekly at one representative site to assess seasonal trends. Ciliates were preserved with Lugol’s iodine; abundance and species composition were determined by standard inverted microscopy. I indicate, using variographic analysis, that the abundance of 4 of the 5 ciliates was neither randomly nor homogeneously distributed, but exhibited structured small and large scale patchy distributions. I indicate that species-specific patterns of patchiness exist in stratified and in mixed waters, supporting the notion of behavioural niche-separation of planktonic ciliates. Patches of <13 m, <18 m, and <77 m were formed by Lohmaniella oviformis, Tintinnopsis sp. and Strombidium sp., respectively. The functional autotroph Myrionecta rubra formed patches of 10, 20, 80, 130, 170, and > 2000 m. In contrast, Pleuronema sp. formed patches below the detection limits of the analysis (<1 m). The total ciliate diversity index was distributed in well-defined patches at different scales within the lagoon, and ranged from 0.1 to 1.9; 37 morphospecies occurred throughout the study. Using geostatistical techniques, I established variograms and used them to model ciliate distribution and predict ciliate behaviour. After analysing the data, I proposed a working definition of a ‘ciliate patch’: regions with abundance above the cut-off of the upper quartile from the kriging prediction model. Error-maps were developed, indicating the coefficient of variation of the predicted distributions. Finally, I speculate on the forces causing patchiness at the 2 scales by examining environmental factors and physiological-behavioural properties of ciliates. This Thesis, thus, has identified previously unknown patterns of ciliates patchiness on both seasonal and spatial scales, by applying a suite of existing statistical techniques and new and innovative statistical techniques that can also be applied to other planktonic groups, and to other fields of ecology. Thus, the work potentially has far reaching implications. Finally, I recommend that new approaches be added to this developing suite of methodologies, and their further application in this field should be directed to understand the functional impact of ciliate patchiness in ecosystems.