Água Santa also had a troublesome off-field relationship with cross-town rivals Clube Atlético Diadema,[3] which resulted in the latter team leaving for Ribeirão Pires.
In 2008, Água Santa played in the Copa Uniligas, an amateur cup contested by the best performing teams in the ABC region.
[5] Água Santa won three consecutive Diadema amateur football league titles from 2009 to 2011, establishing the team as the strongest in the city.
[6] As Diadema was one of the few larger cities in São Paulo that never had a professional football team, the club decided to turn pro, paying a R$600,000 fee to join the Federação Paulista de Futebol, quitting the amateur league in the process.
[6] The Roman god of the sea Neptune was chosen to be the team's mascot due to their name (Holy Water, in Portuguese) and the club's proximity to the Billings dam.
They played their first youth league games undear coach Lilló on 7 April 2014, against local rivals Santo André at Estádio Bruno José Daniel.
[14] Água Santa played their first home game against crosstown rivals and fellow debutant side CAD on 4 May, losing 2–3 in front of a sold-out crowd.
In spite of their local derby defeat, Água Santa's matches kept attracting large crowds and the club eventually won promotion to Série A3 on 13 October, following a 3–1 win against Cotia.
In the 2015 season, Água Santa finished fourth in Campeonato Paulista Série A2, achieving promotion once again, this time to the first tier of the São Paulo state league.
Due to the club's arrival in the top flight, the Estádio Distrital do Inamar had to go through reconstruction, which increased the stadium capacity to 10,000 people.
Água Santa had a decent start to the championship, winning three of the first five games, but soon after the team went into a six-game winless streak, putting Netuno in the relegation zone and resulting in the sacking of long-time manager Márcio Ribeiro after nearly four years in charge of the club.
On 2 April, Água Santa suffered their biggest defeat in history, a 7–2 thrashing by Ponte Preta at Moisés Lucarelli.
[25] A home loss to São Bernardo in the final matchday of the first stage, combined with a Botafogo win over Capivariano officially relegated Água Santa back to the second division for the 2017 season.
With Ribeiro back in charge for the 2019 Campeonato Paulista Série A2, Água Santa returned to good form and finished the first stage at the top of the table.
[45] The new head coach led Água Santa to their first win of the year on 8 February, against Ferroviária, and took the team out of the relegation zone.
[46] On 27 March, with the competition on hold due to the COVID-19 pandemic, Pintado left Água Santa for Brasileirão Série B side Juventude.