Variable climate resulting in floods, and labor-intensive manual rice transplanting are the major challenges in rice cultivation in Assam, India. Our study aimed to improve rice-rice systems productivity through submergence-tolerant rice varieties (STRVs) and mechanical puddled transplanted rice (MTR). On-farm experiments were conducted in four rice seasons over two years (2018-19 and 2019-20) in 15 districts where rice-rice is the dominant cropping system. We evaluated best management practices (BMPs- a combination of STRVs and MTR) against farmers practice (FP-local popular varieties and manual puddled transplanted rice (PTR)). The study also carried out mixed model to assess the unequal distributions of treatments, 127 sites under BMPs and 392 sites under FP. Our results showed that BMPs increased rice grain yield by 25% (1.11–1.14 t ha−1) and net margin by 68–90% (290–320 USD ha−1) over FP across the seasons. The BMPs also had less variable cost by 59–67 USD ha−1 compared to FP. The adoption of BMPs in rice-rice system increased the system productivity by 2.25 t ha−1 and net margin by 610 USD ha−1. We conclude that rice-rice system productivity can be increased by adoption of BMPs in Assam. However, scaling of BMPs requires awareness and access to seeds of submergence-tolerant rice varieties and mechanical transplanters.