Alex has spinal muscular atrophy, a genetic condition that makes his muscles weaker and causes problems with movement.
He is a residential sports student at National Star College for young people with complex disabilities and learning difficulties in Cheltenham, Gloucestershire.
He wanted to be baptised and immersed in water but the challenge was that he needed support to transfer him from his electric wheelchair.
Due to his disability, Mr Smith, from Plymouth in Devon, needed a hoist and specialist support to access a pool.
"Often if a person who has disabilities wants to be baptised, the only way to do it is by covering the wheelchair with plastic protection and pouring water over his head," said Polly White, multi-faith support worker and physiotherapist at National Star.
"But wheelchairs are expensive and Alex wanted to be immersed in water."
Mr Smith worked with the National Star staff and was baptised in the charity's aqua therapy pool on Sunday, watched by family and friends.
Ollie Bennett, pastor of Kingfisher Church in Gloucester which Mr Smith attends, carried out the baptism and admits it was the first one he had ever done in an aqua therapy pool.
"Alex was determined to be baptised in water and it has been a real privilege to be part of this special service," he said.
Mr Smith wrote a speech which he read at the side of the pool before the short service.
"God came to me in my time of need when I felt angry and couldn't express myself in a way that I found appropriate," he said.
"I love coming to church as it is my favourite part of the week. I have been so excited about this service."
Using a hoist, physiotherapists Miss White and her colleague Hattie Neave helped Mr Smith into the aqua therapy pool and supported him during the service.
Listen here to Premier's Cara Bentley speaking to Mat Ray, Head of Church Partnerships at the disability charity Livability:
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