Rovers beat Brentford 3-1 on the final day of the regular season this afternoon, but it was not enough to lift them out of the bottom three as both Birmingham City and Nottingham Forest also won.
Blackburn ultimately went down on goal difference, but Mowbray is hopeful that he can keep the majority of the squad together and bounce straight back next season.
"I am disappointed now but we have to try to keep the spirit we showed here and, if we do, the club will be very strong in League One next year," he told reporters.
"It's decided over 46 games and at the end of the season everyone at the club from the players to the medical team and the analysts have not been good enough to stay in this division. There have been games we've drawn that we should have won, but the harsh reality is if you don't get enough points you can't argue with the outcome.
"We have to take it on the chin. It's going to be a huge summer for us in terms of recruitment, and conversations with the owners are coming - we have to recruit well, be strong next year and bounce back. We need to keep our under-contract players. If we do, we will hopefully be too strong for a lot of clubs in League One. We just need to turn the ship around and get promotion."
Blackburn's relegation means that they are the first Premier League champions to drop into the third tier of English football.