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Alien species have invaded worldwide and altered native biodiversity and ecosystem functions. In Lake Biwa, Japan, Micrasterias hardyi—considered an endemic species in Australia—has become one of the major dominant species since 2016. To evaluate long-term and seasonal variations in M. hardyi, we analyzed 20 years of plankton samples from the northern basin of Lake Biwa. The presence of this species was first confirmed in February 2015, and increased for long periods from November 2015 (4.2 cells cm−2) to December 2016 (2.3 × 105 cells cm−2) and from September 2017 (2.0 × 102 cells cm−2) to January 2019 (5.7 × 104 cells cm−2). Particles similar to chytrid zoosporangia were observed and attached to M. hardyi cells. However, the infection rate was low (up to 22.5%), and the infection did not seem to be a major lethal factor. We estimated that M. hardyi was introduced in the early 2000s by simple linear regression of abundance. This result indicates the existence of long time lag from introduction to detection. Moreover, as the propagule pressure to nearby water systems has been high, it is highly probable that M. hardyi has spread to other lakes and ponds via Lake Biwa. [ABSTRACT FROM AUTHOR]