Schools that used to play the system by entering pupils for exams early and multiple times could be in for a "sharp shock" tomorrow when GCSE results are published, it has been suggested.
Those that relied heavily on "gaming" are more likely to see lower grades, according to Professor Alan Smithers.
His comments come following warnings from England's exams regulator, Ofqual, that there is likely to be "variability" in grades at a school level this summer due to the significant changes to the qualifications.
A move to end-of-course exams, more students taking international GCSEs (IGCSE), cuts to re-sits, a toughening up of GCSE geography, and a decision by Government that only a pupil's first attempt at a GCSE will count in school league tables are all likely to affect this year's results, the regulator said.
Further changes, such as speaking and listening assessments no longer counting towards a student's overall GCSE English grade and a move towards more exams and less coursework in the subject, could also have an impact.
Prof Smithers, director of the Centre for Education and Employment at Buckingham University, said: "Individual schools are likely to be affected differently according to how much they relied on gaming the old system, so for some there could be sharp shocks in store."
Benchmarks set by the Government on the proportions of pupils in each school gaining at least five C grades, including English and maths, have been very important to schools, Prof Smithers said.
"Schools devised all sorts of ways to help the students that might otherwise struggle to meet at least a C grade," he suggested.
This included putting pupils in for exams early to give them practice and allow teachers to identify where pupils were falling short, Prof Smithers said, adding that some schools also used to be "quite generous in assessing speaking and listening".
These methods are no longer possible following the changes to the exams system.
Hundreds of thousands of teenagers across England, Wales and Northern Ireland will be waking up to their GCSE grades tomorrow.
Ahead of the results, teachers' unions called for an end to "untested tinkering" with exams.
Brian Lightman, general secretary of the Association of School and College Leaders (ASCL) said: "The constant piecemeal changes to GCSE exams are making it increasingly difficult for schools to prepare for GCSE exams and to accurately predict what students will achieve.
"Despite constantly shifting exam goal posts, teachers and students have worked incredibly hard to achieve the results that they will receive in the morning.
"If the Government wants to do its part to help young people get the education they need to succeed in life, it must stop this obsession with tinkering with exams."
Nansi Ellis, assistant general secretary for policy at the Association of Teachers and Lecturers (ATL) said: "Continually changing the format of assessments with untested tinkering has to stop. It is not allowing young people to show what they can achieve, nor is it providing them with the skills they need for work and life after school or college."
Last year, the proportion of GCSEs awarded at least a C grade fell for the second year running.
Just over two-thirds (68.1%) of entries scored A*-C, down 1.3 percentage points from 2012 - the biggest fall in the exam's 25-year history.
The proportion of entries gaining top grades also fell by 0.5 percentage points - with 6.8% achieving a coveted A*.
Prof Smithers predicted that this summer could see a slight rise in grades.
"The big drop in early entries, reduction in internal assessment, and the switch from GCSE to iGCSE, is likely to mean fewer weaker candidates this year, so prior attainment could be expected to be higher, and hence a rise in GCSE grades could be anticipated."
Last year's results showed a shift towards pupils studying traditional academic subjects, with an increased number of entries for the three separate sciences, as well as a reversal in the long-term decline of foreign languages.
It was suggested that the hikes could be down to the introduction of the Government's English Baccalaureate (EBacc), which is awarded to pupils who score at least a C at GCSE in English, maths, science, history or geography, and a foreign language.
But there are indications this year that entries numbers in some subjects are unlikely to rise again this year.
Statistics published by the exams regulator Ofqual earlier this year showed that exam entries for biology, chemistry and physics have fallen this year, with biology entries for Year 11 students down 12% to 128,000, chemistry down 11% to 130,000 and physics entries down 9% to 132,000.
But entries for GCSE Science were up 32% to 152,000 and additional science entries were up 18% to 297,000.
The same Ofqual document showed that German entries are down 2%, French has remained static and Spanish has risen 7%.
History entries have increased by 1% and geography is up 4%.
Vicky Gough, schools adviser at the British Council, said: "Provisional figures suggest that the growth we've seen in the number of foreign language exams over the past couple of years has stalled this year. While the introduction of the English Baccalaureate in 2011 gave languages a boost last year, it sadly doesn't look like it's fuelling any more upward momentum.
"The only silver lining is that it would appear that Spanish - which topped the British Council's list of the languages the UK needs the most - has bucked the trend and continues to grow."
Early indications suggest that some schools are seeing turbulence in their results, with particular concerns among some about English and maths.
Mr Lightman said: "We are getting some individual reports of volatility, but we don't know about overall trends yet.
"Some schools have seen surprises. Some schools have seen results which are lower than expected."
One headteacher reported a drop of 18 percentage points in the proportion of students achieving at least a grade C in English.
She told the Times Educational Supplement (TES): "We're absolutely furious. "Our overall results are now below the floor target [of 50% being introduced next year], and it's all down to English. The kids are going to be distraught."
Another said they had seen a "significant drop" in English language A*-C pass rate, and a third told the TES that in maths, the majority of his school's students had achieved "at least one grade lower" than predicted.