Environmental factors and diatoms were studied in 151 stations in Cypriot streams. Since Navicula simplex Krasske [new combination: Craticula simplex (Krasske) Levkov] is based on the small-scale drawing of a single valve and the type material is no longer available, we provide additional ecological, morphological, and ultrastructural data, and an epitype for C. simplex, which is distinguished by valve outline and stria density, and occurs in small, nutrient-enriched streams. Two other symmetric biraphid species are proposed as new to science based on light and scanning electron microscopy, careful comparison with similar established taxa, and on the analysis of our multi-annual databases. Mastogloia cyprica Lange-Bert. et Cantonati sp. nov. differs from similar species by raphe undulation, stria density, and rare occurrence in oligo-to slightly-eutrophic streamlets and lakes with medium-high conductivity. Navicula loumatensis Lange-Bert. et Cantonati sp. nov. is characterized by the combination of valve outline, central area, and by a high areola density, and occurs in medium-high conductivity, low-N but P-enriched streams. In-depth knowledge of Mediterranean stream diatoms is of pivotal importance in these critical decades of climate change.