Mariga started his playing career at Ulinzi Stars before moving first to Tusker FC and then to Kenya Pipeline while still at school. Mariga was a member of the Kamukunji High School 'Golden Boys', which also included Kenyan striker Dennis Oliech (Auxerre, France), who won two consecutive National Championships in 2002 & 2003.
The central midfielder went to Sweden in 2005 to play for third Division side Enköpings SK. After only one season at ESK, he signed for Helsingborgs IF before the 2006 season. His success at Helsingborgs was immediate. Following initial interest from Portsmouth manager Harry Redknapp, Mariga looked set to sign for the Premier League team, but work permit issues held up the deal which was supposed to have cost around €2.7million.
In January 2010 he was set to sign for English club Manchester City of the Premier League, but he failed to obtain a work permit. It was later stated by Kenya's Prime Minister Raila Odinga that 22-year-old Mariga had eventually obtained a UK work permit but only after the transfer window for the Premier League had closed. Had Mariga successfully signed for Manchester City, he would have been the first player from the East African country to sign for a club in the top English league - a milestone later achieved by his brother, upon his transfer to Southampton in July 2013.
On 1 February 2010, the last day of the transfer window, Mariga moved to Inter in a co-ownership deal. The transfer fee was €5 million in a cash plus player deal which Parma got half the registration rights of Jonathan Biabiany (€2.5 million) and the loan of Luis Antonio Jiménez. Following the move, Inter president Massimo Moratti hailed Mariga's move as the "best thing that could have happened" to the club in the January transfer window. He made his debut for Internazionale in the 1st leg of the 2009 Coppa Italia Semi-final against Fiorentina. Inter narrowly won the match 1–0. In March 2010 Mariga became the first Kenyan to play in the UEFA Champions League, when he entered the field as a late substitute against Chelsea.
Mariga thought he scored his first goal for Inter on 24 April 2010 against Atalanta when he netted Samuel Eto'o's back pass into the roof of the net. However his shot deflected off Sulley Muntari and the goal was credited instead to the Ghanaian. He also scored a thrashing header against Genoa for the Nerazzurri in a game that ended 3–2.
On 17 June 2010, Inter bought him outright and bought back Biabiany for €4.2 million each, which made Parma registered a "loss from co-ownership" of €800,000, as the retained profit of unsold half had decreased from €5 million to €4.2 million. However, if counting the profit from Biabiany, which Inter in fact paid Parma €10.9 million cash for Mariga plus the special loan of Biabiany. While Luis Antonio Jiménez originally included in the deal but collapsed after Inter lost its portion on 25 June.
In January 2011 Inter gifted Parma half of the registration rights of Joel Obi for a peppercorn fee but never left Inter, and half of the registration rights of Nwankwo for a price nearly equal to half the price Inter bought him.
At the start of the 2011–12 season Mariga was loaned out to La Liga club Real Sociedad. It meant Inter had a non-EU transfer quota which they used on winter signing Juan and Fredy Guarín (the other quota was obtained from Philippe Coutinho). After half a season back at Inter, he was loaned to Parma in the January 2013 transfer window and he scored his only goal against Lazio. In the next fixture he was injured against Novara, which ruled him out for the rest of the season. He returned to Inter along with Biabiany at the end of the season at the request of manager Andrea Stramaccioni, but was released by the club in May 2014.
Return to Parma
On 4 September 2014, Mariga re-signed with Parma, the team he left to join Inter in 2010.
In January 2016 he was signed by Serie B club Latina.
Mariga scored his first international goal for Kenya against Swaziland on 25 March 2007.
- Serie A: 2009–10
- Coppa Italia: 2010, 2011
- UEFA Champions League: 2009–10
- Supercoppa Italiana: 2010
- FIFA Club World Cup: 2010
Mariga's father, Noah Wanyama, a left winger, played for A.F.C. Leopards and the Kenya national football team. His younger brother Victor Wanyama is also a professional football player, who is currently playing for Premier League side Tottenham, while his other brothers Thomas and Sylvester are also footballers in the Kenyan Premier League. Their younger sister Mercy was the captain of the Lang'ata High School basketball team, and previously played football and netball.
In 2013, Mariga ended his engagement to his long-time Rwandese fiancée Ariane Umutoni, after relations between the couple reportedly deteriorated.