Mehrotra's research expertise is in data management and distributed systems areas in which he has made many pioneering contributions. Two such contributions include the concept of "database as a service" and "use of information retrieval techniques, particularly relevance feedback, in multimedia search". Mehrotra is a recipient of numerous best paper nominations and awards including SIGMOD Best Paper award in 2001 for a paper entitled "Locally Adaptive Dimensionality Reduction for Indexing Large Time Series Databases", Best of VLDB 1994 submissions for a paper entitled "Concurrency Control in Hierarchical Multidatabase System", best paper award in DASFAA 2004 for the paper entitled "Efficient Execution of Aggregation Queries over Encrypted Databases", best paper award nomination for a paper entitled Neighborhoods: A framework for enabling web-based synchronous collaboration and hierarchical Navigation at HIICS, 1996, and a best student paper award at IEEE Workshop on Multimodal Sentient Computing: Sensors, Algorithms and Systems (WMSC 2007) held in conjunction with IEEE CVPR (Computer Vision and Pattern Recognition) 2007.

Mehrotra's current research focuses on building sentient spaces using multimodal sensors, data privacy, and data quality. Mehrotra's recent research, particularly, in the context of RESCUE & CERT has focused on situational awareness from multimodal input including conversational speech data. Many of his research contributions have been incorporated into software artifacts which are now in use at various first responder partner sites.