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from sqlalchemy.interfaces import ConnectionProxy
import time

import logging
log = logging.getLogger(__name__)

class TimerProxy(ConnectionProxy):
    def cursor_execute(self, execute, cursor, statement, parameters, context, executemany):
        now = time.time()
        try:
            return execute(cursor, statement, parameters, context)
        finally:
            total = time.time() - now
            log.debug("Query: %s" % statement)
            log.debug("Total Time: %f" % total)

config/environment.py:

engine = engine_from_config(config, 'sqlalchemy.', proxy=TimerProxy())