Global aquaculture production continues to grow to meet the high demand for fish food by the ever-increasing population worldwide. In particular, the Malaysian aquaculture sector produced approximately 411,781 tonnes of total aquaculture production with an estimated economic value of USD 700 million in 2019. However, this industry in Malaysia faces many challenges that hinder future development, especially in sustaining this industry. This is mainly due to the lack of motivation to meet the sustainability criteria. Therefore, the aquaculture industry is under immense pressure to embrace sustainability measures due to concerns about environmental impacts. Therefore, this article outlines the production and value of common cultivable species in Malaysia for freshwater and brackish water aquaculture and the intensification and development of the aquaculture industry in Malaysia. This review also thoroughly discussed various sustainable challenges such as waste generation, the use of chemicals and drugs, the outbreak of diseases, and others related to the aquaculture industry. In contrast, it also highlighted many opportunities, such as the expansion of extractive species aquaculture, the conversion of aquaculture waste into value-added products, and aquaculture tourism to pursue a sustainable aquaculture industry in Malaysia. Hence, this comprehensive review will positively impact the future development of the aquaculture industry in the global context, particularly in Malaysia.