Changes to GCSE entry patterns, along with new maths qualifications, have 'substantially' impacted on this year's grades - according to the WJEC.
The top grade A* remains stable, but there has been a fall in grades A*-C.
The exam board says there are several factors this year affecting the results in different ways for individual subjects.
These include six new GCSE qualifications, as well as the new Skills Challenge Certificate for the Welsh Baccalaureate.
This year also sees a substantial entry by year 10 students, who are in their first year of the two-year course, in some of the new GCSEs.
The headline outcomes are as follows:
- English Language: A slight improvement in results for 16-year-olds, and a very large number of entries by 15-year-olds.
- Welsh (1st) Language: Stable outcomes for 16-year-olds and more entries by 15-year olds.
- Welsh Literature: A small improvement in outcomes, but a substantial fall in entries.
- English Literature: An improvement in outcomes but very large fall in entries.
- Mathematics: Results across the academic year are stable at grades A* and A, but there has been a fall across A*-C.
- Mathematics – Numeracy: Nearly 60% of candidates achieved A*-C in the academic year for this new qualification.
- Welsh (2nd) Language: Improved results at A* and A*-A for full course, with an increase in entries.
- Sciences: An increase in entries for separate sciences, but a fall in outcomes.
- Modern Foreign Languages: Slight increase in entries for Spanish, but a fall in French and German.
Wales' Education Secretary Kirsty Williams congratulated pupils on their results, but expressed concern over the high number of pupils being entered early for GCSE exams.
She said: “I am concerned about the high number of pupils being entered early for their exams. Many of these pupils, who are taking exams before they have completed their two years of GCSE study, have not had the opportunity to reach their full potential. This is putting unnecessary pressure on pupils, teachers and also puts an extra strain on school budgets.
"I will respond to Qualifications Wales’s rapid review of this issue when I receive it in October, but the current situation is unsustainable and all options are on the table."
Meanwhile, pupils across Wales have been celebrating their results.