Industry, agriculture, and residential areas generate increasing volumes of waste streams enriched with organic pollutants. Without proper treatment, they threaten the environment, but can be valorized with suitable microalgal biotechnologies. Although their development has a long history, recent years are marked with a boom of research in this field. This trend is fueled by the transition to circular bioeconomy gaining momentum all over the world. Current trends include the conversion of nutrients, including organics, nitrogen, and especially phosphorus from waste streams to environmentally friendly biofertilizer, detoxication of dangerous xenobiotics (pesticides and antibiotics), as well as the implementation of advanced omics methods for monitoring of treatment and designing of robust algal–bacterial consortia. Here, we review the recent developments highlighting the trends mentioned above.