Paleoecology attempts to reconstruct history through geochemical isotopic studies, trace fossil analyses, examination of microbe communities, and the presence or lack of microfossils. Ancient lakes are useful for reconstructing paleoecology because they accumulate sediment through time. Paleobotanical microfossils, including diatoms and phytoliths, allow inference of vegetation, pH, salinity, water chemistry, and environmental temperature, among others. Here, we propose a protocol split into two sections to prepare slides and count diatoms and phytoliths along transects. Researchers can develop an ecological history by analyzing microfossils from different locations and times. As an example, we apply this method to study the palaeobotanical microfossils of an 820 cm deep stratigraphy, composed of 10.3my Miocene diatomite, from a high-elevation desert paleolake in Northern Nevada (Fernley District). The preliminary results hint at a complex climatic and environmental variance. Another application of this method includes the development of environmental interpretations and hypotheses regarding the future of modern vegetation.