The community structures of phytoplankton are important factors and indicators of lake water quality. Harmful algal blooms severely impact water supply, recreational activities and wildlife habitat. This study aimed to examine the phytoplankton composition and variations using microscopy, and identify harmful Cyanobacteria in weekly samples taken from four sites at Harsha Lake in southwest Ohio. Over the course of the summer in 2015, the phytoplankton of Harsha Lake consisted mainly of 13 taxa belonging to Bacillariophyta, Chlorophyta, Cryptophyta, Cyanobacteria, Dinophyta and Euglenophyta. Their significant successions started with Bacillariophyta and/or Chlorophyta, then bloomed with Cyanobacteria and ended with Chlorophyta and/or Dinophyta. Cyanobacteria members: Microcystis, Planktothrix, Dolichospermum, Aphanizomenon, Cylindrospermopsis, and Oscillatoria from the Cyanophyceae were identified to be dominant genera. These organisms varied spatially and temporally in similar patterns along with the variations of nutrients and formed the summer bloom with the total biomasses ranging from 0.01 to 114.89 mg L−1 with mean of 22.88 mg L−1. M. aeruginosa and P. rubescens were revealed as the microcystin producers, while A. circinalis and Aphanizomenon sp. were identified as a saxitoxin producer through cloning and sequencing PCR products of mcyA, mcyE and sxtA genes. The biomasses of phytoplankton, Cyanobacteria and Microcystis were positively correlated to nutrients, especially to total nitrogen. The total ELISA measurement for microcystin positively correlated with Cyanobacteria (R2 = 0.66, P < 0.0001), Microcystis (R2 = 0.64, P < 0.0001) and phytoplankton (R2 = 0.59, P < 0.0001). The basic information on the occurrence and biomasses of Cyanobacteria and total phytoplankton, and the analysis for toxic species, which were the first report for the inland water in Ohio, USA, will document the succession patterns of phytoplankton and toxin production over a season and provide data to predict risk occurrence to both human and ecological factors.